X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=fe11da29e3bd285066fc3cb41cf80717c7b0cfc1;hb=fc236a11b6b6ace1cb5ee572dded25a9dec07496;hp=a3008fc54a531093200dd1b61960bf040a48cee8;hpb=2594fb7e8055fefc08b37a14ad437aa9bafbe837;p=samtools.git

diff --git a/padding.c b/padding.c
index a3008fc..fe11da2 100644
--- a/padding.c
+++ b/padding.c
@@ -57,7 +57,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
 	bam_header_t *h;
 	bam1_t *b;
 	kstring_t r, q;
-        int r_tid = -1;
+	int r_tid = -1;
 	uint32_t *cigar2 = 0;
 	int n2 = 0, m2 = 0, *posmap = 0;
 
@@ -76,6 +76,10 @@ int bam_pad2unpad(bamFile in, bamFile out)
 			*/
 			r_tid = b->core.tid;
 			unpad_seq(b, &r);
+			if (h->target_len[r_tid] != r.l) {
+				fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+				return -1;
+			}
 			write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
 			replace_cigar(b, n2, cigar2);
 			posmap = realloc(posmap, r.m * sizeof(int));
@@ -93,7 +97,17 @@ int bam_pad2unpad(bamFile in, bamFile out)
 				return -1;
 			}
 			unpad_seq(b, &q);
-			if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+			if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[0]);
+			} else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[0]);
+				if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+					write_cigar(cigar2, n2, m2, cigar[1]);
+				}
+			} else {
+	  			/* Insert a dummy 0M entry to let use remove superfluous leading P ops */
+				write_cigar(cigar2, n2, m2, 0);
+			}
 			/* Include any pads if starts with an insert */
 			for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
 			if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
@@ -108,11 +122,34 @@ int bam_pad2unpad(bamFile in, bamFile out)
 				} else ++k;
 			}
 			write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
-			if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
-			/* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
+			if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+                        } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+				if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+					write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+			  	}
+				write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+			}
+			/* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
+			/* or right at the start before M/X/=/D */
+			int pre_op, post_op;
 			for (i = 2; i < n2; ++i)
-				if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
-					cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
+				if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+					pre_op = bam_cigar_op(cigar2[i-2]);
+					post_op = bam_cigar_op(cigar2[i]);
+					/* Note don't need to check for X/= as code above will use M only */
+					if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF || pre_op == BAM_CSOFT_CLIP || pre_op == BAM_CHARD_CLIP) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
+						/* This is a redundant P operator */
+						cigar2[i-1] = 0; // i.e. 0M
+						/* If had same operator either side, combine them in post_op */
+						if (pre_op == post_op) {
+							/* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+							cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+							cigar2[i-2] = 0; // i.e. 0M
+						}
+					}
+				}
+			/* Remove the zero'd operators (0M) */
 			for (i = k = 0; i < n2; ++i)
 				if (cigar2[i]) cigar2[k++] = cigar2[i];
 			n2 = k;